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Course overview: The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent.
eBioKit is a system for teaching bioinformatics, which is running multiple open source web services on an Apple Mac-mini where all databases are stored locally. This reduces the need for a fast internet connection while giving the users an opportunity to incorporate their data sets in widely used web services.
This course is aimed at familiarizing trainees with the multiple uses of ebiokit. The course will train members who are required to perform bioinformatics analysis of genetic and genomic data generated in the various H3Africa projects but most likely also in other projects in there respective institutions.
The course will be 5 days long and will cover both theoretical and practical aspects of a range of topics centered on the analysis of genetic and genomic data. An emphasis will be placed on allowing participants to develop hands-on experience with analyzing real data using ebiokit.
The course is open to all members of the H3A Bioinformatics Network as well as H3A Researchers who are seeking advanced bioinformatics training.
The course is composed of a range of topics aimed at providing participants with the necessary hands-on practical skills to be able to analyze genetic, genomic and metagenomic data. The course will include some basic linux programming and then offer a comprehensive overview of commonly used bioinformatics tools and databases available on the eBiokit system, such as for example Ensembl and Galaxy, a Web-based platform for data-intensive biomedical research.
Prof. Erik Bongcam-Rudloff, SLU-Global Bioinformatics Centre, Sweden
Dr. Andreas Gisel, Institute for Biomedical Technologies, Italy
Dr. Anne Fischer, ICIPE, Kenya
Dr. Etienne de Villiers, KWTRP, Kenya
Rafael Hernández, Centro de Investigaciones Príncipe Felipe
Introduction to Bioinformatics
How to use the eBioKit
UNIX command line
Introduction to Biological Databases
Basics of Blast search
Constructing your own searchable blast database
MRS: searching with names and keywords
Introduction to Genome Browsers: Ensembl: part 1
Exploring ENSEMBL functionalities: part 2
EMBOSS (the European Molecular Biology Open Software Suite):
Alignments, global, local
Searching with motifs and more
Multiple alignments
Introduction to Phylogenetics
Introduction to the Galaxy platform
NGS data quality control
NGS genome mapping/SNP analysis
NGS RNA-seq
NGS Metagenomic data analysis
Using a Bioinformatics "Graphic User Interface"
Training Materials Availability:
Training materials for this course are not currently available.
The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. The H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent. To achieve this vision the H3ABioNet will be hosting the first specialized bioinformatics training course for bioinformaticians and researchers within the network.
The course is aimed at developing a core set of specialised skills amongst members in the network who are in a position to train others at their institutions. The course will train members who are required to efficiently manage and analyse the vast amount of genomic data generated by the various H3Africa projects.
The course will be run over 3 weeks (6 days a week) and will cover both theoretical and practical aspects of a range of topics centered on the analysis of genomic and population-based data. An emphasis will be placed on allowing participants to develop hands-on experience with analysing real data using open source software, tools and resources.
The course is open to all members within the H3A Bioinformatics Network, who have long term positions at one of the partner institutions and the capacity to train others in their institution when they return from the course.
The course is composed of a range of topics aimed at providing participants with the necessary hands-on practical skills to be able to manage and analyse genomic data. As well as specialized topics in population genetics, GWAS and next-generation sequence analysis, the course will include programming to ensure participants gain basic skills in data manipulation and management, and biostatistics to prepare them for statistical analysis of data.
Programming using python – basic introduction through to advanced topics for managing and manipulating biological data. Will be run for 2 hours every morning for the duration of the course.
Introduction to Linux – basic history and introduction through to complex commands for manipulating data and Bash scripting
Data management – building simple MySQL queries and introduction to BioMart
Biostatistics – basic probability theory, introduction to R, statistical hypothesis testing, principal component analysis, building regression models and visualisation
Population genetics – content to be confirmed
Genome-wide association studies – content to be confirmed
Next-generation sequencing – introduction and QC, assembly and reference genome alignment, variant calling, RNA-seq data analysis, ChIP-seq data analysis, genome visualisation
Each course component will have prerequisites that participants will be required to complete or fulfill before the course starts. Participants will be notified of these requirements before the course commences.
To apply to attend the course please complete the application form found here:
http://surveys.h3abionet.org/icipe
The deadline for applications is the 17th May 2013.
Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached.
For those who are unable to attend the course in person, there will be the possible option of joining the course via live streaming to Tunis (Institut Pasteur) and IBADAN (NABDA-Southwest Center, University of Ibadan).
Training Materials Availability:
Training materials for this course are not currently available.
The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. The H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers, but also to build local expertise and infrastructure. To achieve this, H3ABioNet will be hosting a short workshop on NIH grants management.
The course will be run over 2 days, and will be open to members of the H3A Bioinformatics Network, who are involved in the management of the H3ABioNet grant at each partner institution. It will be run by the NHGRI grant officials: Chris Darby and Lisa Oken.
To apply to attend the course please complete the application form found here:
http://surveys.h3abionet.org/grantscourse/
Please ensure that all required information is completed on the application. The deadline for applications is the 10th May 2013.
Training Materials Availability:
Training materials for this course are not currently available.
Workshop training materials are available at: http://training.h3abionet.org/technical_workshop_2013/
The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent.
In order to prepare for the large amount of data that will be generated by the various projects, the initial requirement is to set up the required computational infrastructure and resources to store, manage the data. To address this requirement, the H3ABioNet will be hosting a technical training course for H3ABioNet-funded staff and students.
The objective of the two-week training course is to equip H3ABioNet technical staff and students at the partner sites with the skills required to set up and maintain the necessary computational infrastructure and resources. The course will be both theoretical and practical, with an emphasis placed on hands-on experience in setting up and maintaining these resources. The course is aimed at individuals with a computational science background.
Linux installation and system administration
Galaxy installation, configuration and optimisation
High performance computing, optimisation for genomic applications
Security and data stewardship, firewalls, intrusion detection, data backups and archives, encryption, data privacy
Data management, GridFTP, Globus Online, database design, web interfaces
Genome databases, CHADO and BioMart,
Data Visualisation, genome browsers, trackster and DAS
Cloud computing, basic concepts, cloud services, creating virtual machines, deploying software environments, CloudMan, genome browsers
The course will have prerequisites that participants will be required to complete or fulfill before the course starts. Participants will be notified of these requirements before the course commences. The minimum requirement is a computer science/IT background with some Unix and programming experience.
To apply to attend the course please complete the application form found here:
http://surveys.h3abionet.org/sysadmincourse
Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached. The deadline for applications is the 10th May 2013
Day 1 of Workshop: https://youtu.be/
Day 2 of Workshop: https://youtu.be/
Resources:
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Tools and Services
Resources
Communication